2 Answers
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I found these instructions on a forum. After several tries, I was able to get both the ignition and keyless entry to work.

Make sure you have on your original key and have looked on the back for a black toyota logo. This WILL NOT work for the smart keys with the SILVER toyota logo.

(Yes it Does for a 2009 Prius. Also BIG Thing: Have only the old remote and new or USED remote in the car. No Cell or Phone or Blue Tooth)

Insert old fob into slot and remove it 4 times in a row, and insert it a fifth time but leave it in there!

Open and close driver door 6 times.

Remove old fob from slot. Car is in fob programming mode at this point.

Insert new fob and leave in the slot for a full minute. Watch the blinking red anti-theft light on the dashboard. When it stops flashing and goes dark, your new fob is all set.

After a minute, press the power once and open door, or vise-vera, Hey it worked for me, but only with the FOB inserted.

Remove the new fob and you're done. You should test both fobs to be sure they work properly.

Now for the door lock functions.

The Fob (for remotely unlocking/locking the doors)

Open the driver door with no fob in slot and the driver door unlocked and opened. Other doors can be locked or unlocked, it doesn't matter.

Insert old fob into slot and remove it twice within 5 seconds.

Close and open driver door twice.

Insert and remove old fob once.

Close and open driver door twice again.

Insert old fob in slot and close door.

Without pressing the brake, press power button, wait a second, press it again, wait a second, press it a third time to turn car back off.

Remove old fob from slot. You'll be in "add mode" at this point.

Car should lock and unlock doors TWICE to verify it is in add mode.

Press both buttons on new fob simultaneously for a second and a half!.
11 Within 3 seconds, press only the lock symbol button. yes it does matter which!

Car should respond with one quick lock/unlock to verify that the new fob is all set. If the car responds with two lock/unlocks, that means it didn't work. I don't know how to troubleshoot that problem. Maybe just try again.

To end this programming, open a door or put fob in the slot.

Enjoy the savings from NOT buying a fob from the dealership!!!!!

If you want metal keys, DO not buy them from ebay, they quoted me $7.92 CUT by them from dealer.

There is a difference between an "OEM" new never programmed FOB and on that has already been linked to a vehicle. That being said there is hope if you have gotten one off EBay that was used. The directions to program the ability to start the car work fine on either the OEM or the used FOB but the smart key (SKS) functions will not program with the open-close-door dance on a used FOB. All 4 of the Toyota dealers that I called told me there was nothing I could do and offered to sell me a new FOB and program it for prices ranging from $230-$290.
A locksmith saved the day. There is a device called a T-Code pro that plugs into the OBDII port on the Prius (I have a 2008) and allows the locksmith to reset the immobilizer (takes 16 min) after the reset ALL FOBs have to be programmed into the system (even an existing one that worked). This is as simple as holding both the lock and unlock buttons on the FOB for a second or two. The car will beep and ta-da the $60 used FOB now works for both the ignition and the SKS. I am sure prices will vary but the locksmith that I found only charged $50 for the service (I brought the car to him so no travel fee). So for about $110 I now have two FOBs with complete functionality, one original to the car and one “used” one from EBay.
I hope this helps other owners that, like me are just trying to save a buck.